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Phylogenetic analysis and molecular evolution patterns in the MIR482-MIR1448 polycistron of Populus L.

Zhao JP, Diao S, Zhang BY, Niu BQ, Wang QL, Wan XC, Luo YQ - PLoS ONE (2012)

Bottom Line: Furthermore, by comparing the substitution patterns in the miRNA-target complexes of miR482 and miR1448, we inferred that co-evolution between miRNAs and their targets was the major force that drove the "duplicated MIR482" evolve to MIR1448.We propose a novel miRNA-target pairing pattern called the "frameshift targeted mechanism" to explain the gain of target genes by miR1448.The results also imply that the major role of miR482 was in resistance to disease or other stresses via NBS-LRR proteins, whereas the biological functions of miR1448 are more diverse.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Tree Genetics and Breeding, Institute of New Forestry Technology, Chinese Academy of Forestry, Beijing, China. zhaojiaping@gmail.com

ABSTRACT
The microRNAs (miRNAs) miR482 and miR1448 are disease resistance-related miRNAs; the former is ubiquitously distributed in seed plants whereas the latter has only been reported in Populus trichocarpa. The precursor and mature sequences of poplar miR1448 are highly homologous to those of poplar miR482, and these two miRNAs are located in one transcript as a polycistron. Therefore, we hypothesized that the MIR1448 gene may have evolved from the MIR482 gene in poplar. However, the molecular evolution patterns of this process remain unclear. In this study, utilizing cloning and Blast analysis in NCBI ESTs and whole-genome shotgun contigs (WGS) dataset, we determined that the MIR482-MIR1448 polycistron is a family-specific clustered miRNA in Salicaceae. Moreover, phylogenetic analysis illustrated that MIR1448 is the product of a tandem duplication event from MIR482. Nucleotide substitution analysis revealed that both MIR482 and MIR1448 have more rapid evolution ratios than ribosomal DNA (rDNA) genes, and that compensatory mutations that occurred in the stem region of the secondary structure were the main mechanisms that drove the evolution of these MIRNA genes. Furthermore, by comparing the substitution patterns in the miRNA-target complexes of miR482 and miR1448, we inferred that co-evolution between miRNAs and their targets was the major force that drove the "duplicated MIR482" evolve to MIR1448. We propose a novel miRNA-target pairing pattern called the "frameshift targeted mechanism" to explain the gain of target genes by miR1448. The results also imply that the major role of miR482 was in resistance to disease or other stresses via NBS-LRR proteins, whereas the biological functions of miR1448 are more diverse.

Show MeSH
The tertiary structure of miR482-miR1448 polycistron in Populus trichocarpa.The MFE structure prediction used RNAstructure v5.3 showed that the pre-miR482 and pre-miR1448 could form a stem-loop structure, meanwhile, the internal region in miR482-miR1448 polycistron also could fold back on itself to form a helix.
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pone-0047811-g004: The tertiary structure of miR482-miR1448 polycistron in Populus trichocarpa.The MFE structure prediction used RNAstructure v5.3 showed that the pre-miR482 and pre-miR1448 could form a stem-loop structure, meanwhile, the internal region in miR482-miR1448 polycistron also could fold back on itself to form a helix.

Mentions: There was no difference in the substitution ratio between pre-miR482 and pre-miR1448. However, as mentioned above, the mutation ratio of the internal region was clearly lower than that of the functional regions, and similar to that of rDNA regions (Table 2). Recently, Chakraborty et al. (2012) also found that the internal regions in miR-17-92a polycistron are significantly conserved. Moreover, structure analysis shown that the internal regions in miRNAs polycistron, such as that in miR-17-92a polycistron [15], Osa-miR395 and ath-miR774-miR859 polycistron [10], could fold back on itself to form a helix. The MFE structure of poplar MIR482-MIR1448 polycistrons were predicted in this study. The results also revealed that the internal regions could form a stable stem-loop structure (Figure 4). Therefore, we inferred that these internal regions might have an crucial role in poplar trees. Therefore, we assumed the MIR482-MIR1448 internal region was not only the union of the two precursors, but with some crucial role in miRNA maturation.


Phylogenetic analysis and molecular evolution patterns in the MIR482-MIR1448 polycistron of Populus L.

Zhao JP, Diao S, Zhang BY, Niu BQ, Wang QL, Wan XC, Luo YQ - PLoS ONE (2012)

The tertiary structure of miR482-miR1448 polycistron in Populus trichocarpa.The MFE structure prediction used RNAstructure v5.3 showed that the pre-miR482 and pre-miR1448 could form a stem-loop structure, meanwhile, the internal region in miR482-miR1448 polycistron also could fold back on itself to form a helix.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3475693&req=5

pone-0047811-g004: The tertiary structure of miR482-miR1448 polycistron in Populus trichocarpa.The MFE structure prediction used RNAstructure v5.3 showed that the pre-miR482 and pre-miR1448 could form a stem-loop structure, meanwhile, the internal region in miR482-miR1448 polycistron also could fold back on itself to form a helix.
Mentions: There was no difference in the substitution ratio between pre-miR482 and pre-miR1448. However, as mentioned above, the mutation ratio of the internal region was clearly lower than that of the functional regions, and similar to that of rDNA regions (Table 2). Recently, Chakraborty et al. (2012) also found that the internal regions in miR-17-92a polycistron are significantly conserved. Moreover, structure analysis shown that the internal regions in miRNAs polycistron, such as that in miR-17-92a polycistron [15], Osa-miR395 and ath-miR774-miR859 polycistron [10], could fold back on itself to form a helix. The MFE structure of poplar MIR482-MIR1448 polycistrons were predicted in this study. The results also revealed that the internal regions could form a stable stem-loop structure (Figure 4). Therefore, we inferred that these internal regions might have an crucial role in poplar trees. Therefore, we assumed the MIR482-MIR1448 internal region was not only the union of the two precursors, but with some crucial role in miRNA maturation.

Bottom Line: Furthermore, by comparing the substitution patterns in the miRNA-target complexes of miR482 and miR1448, we inferred that co-evolution between miRNAs and their targets was the major force that drove the "duplicated MIR482" evolve to MIR1448.We propose a novel miRNA-target pairing pattern called the "frameshift targeted mechanism" to explain the gain of target genes by miR1448.The results also imply that the major role of miR482 was in resistance to disease or other stresses via NBS-LRR proteins, whereas the biological functions of miR1448 are more diverse.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Tree Genetics and Breeding, Institute of New Forestry Technology, Chinese Academy of Forestry, Beijing, China. zhaojiaping@gmail.com

ABSTRACT
The microRNAs (miRNAs) miR482 and miR1448 are disease resistance-related miRNAs; the former is ubiquitously distributed in seed plants whereas the latter has only been reported in Populus trichocarpa. The precursor and mature sequences of poplar miR1448 are highly homologous to those of poplar miR482, and these two miRNAs are located in one transcript as a polycistron. Therefore, we hypothesized that the MIR1448 gene may have evolved from the MIR482 gene in poplar. However, the molecular evolution patterns of this process remain unclear. In this study, utilizing cloning and Blast analysis in NCBI ESTs and whole-genome shotgun contigs (WGS) dataset, we determined that the MIR482-MIR1448 polycistron is a family-specific clustered miRNA in Salicaceae. Moreover, phylogenetic analysis illustrated that MIR1448 is the product of a tandem duplication event from MIR482. Nucleotide substitution analysis revealed that both MIR482 and MIR1448 have more rapid evolution ratios than ribosomal DNA (rDNA) genes, and that compensatory mutations that occurred in the stem region of the secondary structure were the main mechanisms that drove the evolution of these MIRNA genes. Furthermore, by comparing the substitution patterns in the miRNA-target complexes of miR482 and miR1448, we inferred that co-evolution between miRNAs and their targets was the major force that drove the "duplicated MIR482" evolve to MIR1448. We propose a novel miRNA-target pairing pattern called the "frameshift targeted mechanism" to explain the gain of target genes by miR1448. The results also imply that the major role of miR482 was in resistance to disease or other stresses via NBS-LRR proteins, whereas the biological functions of miR1448 are more diverse.

Show MeSH